Chances are this exact same thing is going on here: the font version is stored as a floating-point number? If I’m right, then there’s nothing you can do except change the version number to almost anything else than 1.001.
The fontRevision is stored as a “32-bit signed fixed-point number (16.16)” (google it, this is a lot of fun). And I had another look at my code and it turns out, there was a rounding problem like this already. I fixed it. Thanks for bringing this up.